scout-browser 4.98.0__py3-none-any.whl → 4.99.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- scout/adapter/mongo/institute.py +42 -55
- scout/adapter/mongo/variant.py +19 -15
- scout/adapter/mongo/variant_loader.py +11 -11
- scout/build/individual.py +2 -0
- scout/build/variant/variant.py +8 -0
- scout/commands/download/ensembl.py +18 -2
- scout/commands/update/individual.py +2 -0
- scout/commands/update/panelapp.py +15 -2
- scout/constants/__init__.py +6 -7
- scout/constants/clnsig.py +2 -0
- scout/constants/file_types.py +12 -0
- scout/constants/igv_tracks.py +8 -6
- scout/constants/panels.py +3 -0
- scout/constants/variant_tags.py +6 -6
- scout/demo/643594.config.yaml +1 -0
- scout/load/panelapp.py +11 -5
- scout/models/case/case_loading_models.py +4 -0
- scout/parse/variant/clnsig.py +38 -0
- scout/parse/variant/genotype.py +4 -10
- scout/parse/variant/models.py +5 -11
- scout/parse/variant/rank_score.py +5 -13
- scout/parse/variant/variant.py +90 -111
- scout/server/app.py +33 -22
- scout/server/blueprints/alignviewers/controllers.py +29 -10
- scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html +41 -11
- scout/server/blueprints/cases/templates/cases/utils.html +6 -6
- scout/server/blueprints/clinvar/controllers.py +29 -14
- scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html +13 -4
- scout/server/blueprints/clinvar/views.py +14 -2
- scout/server/blueprints/institutes/controllers.py +10 -2
- scout/server/blueprints/login/controllers.py +112 -12
- scout/server/blueprints/login/views.py +38 -60
- scout/server/blueprints/public/templates/public/index.html +5 -1
- scout/server/blueprints/variant/controllers.py +1 -1
- scout/server/blueprints/variant/templates/variant/acmg.html +6 -2
- scout/server/blueprints/variant/templates/variant/components.html +19 -0
- scout/server/blueprints/variant/templates/variant/utils.html +3 -3
- scout/server/blueprints/variants/controllers.py +10 -1
- scout/server/blueprints/variants/templates/variants/components.html +28 -0
- scout/server/blueprints/variants/templates/variants/mei-variants.html +8 -6
- scout/server/blueprints/variants/templates/variants/sv-variants.html +9 -7
- scout/server/blueprints/variants/templates/variants/utils.html +8 -12
- scout/server/blueprints/variants/templates/variants/variants.html +4 -25
- scout/server/config.py +8 -0
- scout/server/utils.py +22 -5
- scout/utils/acmg.py +25 -26
- scout/utils/ensembl_biomart_clients.py +1 -1
- scout/utils/ensembl_rest_clients.py +25 -32
- scout/utils/hgvs.py +1 -1
- {scout_browser-4.98.0.dist-info → scout_browser-4.99.0.dist-info}/METADATA +10 -14
- {scout_browser-4.98.0.dist-info → scout_browser-4.99.0.dist-info}/RECORD +54 -54
- {scout_browser-4.98.0.dist-info → scout_browser-4.99.0.dist-info}/WHEEL +0 -0
- {scout_browser-4.98.0.dist-info → scout_browser-4.99.0.dist-info}/entry_points.txt +0 -0
- {scout_browser-4.98.0.dist-info → scout_browser-4.99.0.dist-info}/licenses/LICENSE +0 -0
@@ -16,7 +16,7 @@ scout/adapter/mongo/filter.py,sha256=rIdjiDJCrNDeTNgssKm7n1HTxne72jvlX2I3FQjQGo8
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scout/adapter/mongo/hgnc.py,sha256=P80WdIFkpFDeR6Pa0H-pgeScGrZdCviWVL4rqR5Aqvk,16547
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scout/adapter/mongo/hpo.py,sha256=ps2Pix3sGeea7DenboZVP5j7Vh9WAgX3-sgpbAj0Eck,6871
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scout/adapter/mongo/index.py,sha256=TZPVv6xBWsEtZpBUWp5uhjuPjQMfVss4lZZju49g1Lw,3577
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scout/adapter/mongo/institute.py,sha256=
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scout/adapter/mongo/institute.py,sha256=SaA1mRxIZHtMfriMnd0yKiup-xSAG5g0ry9Achra9Tk,6646
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scout/adapter/mongo/managed_variant.py,sha256=mPbp64nMDwAij8zvBbFGjI3MLbk6CC-OO9RTwtEIi44,8451
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scout/adapter/mongo/matchmaker.py,sha256=amTvFOlUbrt1RmecY_8hPY6bO3j79lc2UbmzlCQcRuk,6378
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scout/adapter/mongo/omics_variant.py,sha256=rgfHZYElFDNeh9Atx-oNhS3PbKbiDWn4JABGPZ33Vzk,8024
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@@ -26,16 +26,16 @@ scout/adapter/mongo/query.py,sha256=DqgpPGm9n3lmReHfVMGUNVCTvvMltRXSzaeYW5tDaXc,
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scout/adapter/mongo/rank_model.py,sha256=wvDNI4OLf-f7ZYZ_Q_6qi0myxOJCNNJR_-2-_0u2K2M,5712
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scout/adapter/mongo/transcript.py,sha256=3U1qtyxZ1DnrzdBJm_emJXISMYFKJuX_zAKynUt8NMY,7417
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scout/adapter/mongo/user.py,sha256=QoQnRWqi_dV3ZwGzBonEU6Ap9TgMDf2x_C5UIqG0pa0,2569
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scout/adapter/mongo/variant.py,sha256=
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scout/adapter/mongo/variant.py,sha256=qejO1Su7vR_6z94meEW9kt-MHQEQeAoFhBc98LUvrTE,35530
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scout/adapter/mongo/variant_events.py,sha256=yNnMM58P1LbYFw73rWzti6l2zWa_G93ozUTbVkcz4_I,33475
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scout/adapter/mongo/variant_loader.py,sha256=
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scout/adapter/mongo/variant_loader.py,sha256=H0khshP5i9od-UTPzlRejMoL_CNZlT8jXtqBZ_sWctc,28257
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scout/build/__init__.py,sha256=GUWEaXTpwsJil_KtrXBQJpZIwCQFSgo8NlK49R9IkA8,521
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scout/build/acmg.py,sha256=M21MrrP_dtEyOuu6t-jBDdaqYcHPMLcwJlt9fHG2ycE,1523
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scout/build/case.py,sha256=LtYx6zQcCoGCss48qf7uluzTlXVH0Pl-WhqYzkbIcZ8,11510
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scout/build/ccv.py,sha256=cfAWSQ5cSBWURkL9_fPm1Y5aRcTIDOE9ieSWaYLufB4,1660
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scout/build/disease.py,sha256=Zew9AF_z1NbbKcO3uJZ2wgni501SkfnYRgnaCZ4m8FY,2020
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scout/build/hpo.py,sha256=LJBCTq-x09D0CSKcUHB8a6ynuUrVh_7Ia0ooA1BxMys,1207
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scout/build/individual.py,sha256=
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scout/build/individual.py,sha256=6Lg3ty8gdEG2O9BioDk_Fd9mAXb9QgibSzB7IRLTPJk,5195
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scout/build/institute.py,sha256=CZKn-cFbh0cWO2ySoRV_P1nYFizlyvu50LKrtAz-PLo,1330
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scout/build/managed_variant.py,sha256=krcQBc4LLxlnUQwXuV2FxNLiSkMoIkLxQueYFl04Vyo,1666
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scout/build/panel.py,sha256=smhtynG_ggNgUyuAGqg_-m1UMnBHhrk2ALutYoNTTec,4273
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@@ -50,7 +50,7 @@ scout/build/variant/compound.py,sha256=tYikQ4PmgAH1_yrE9uYaUX4_EoAs_XEiT8JWAjrZu
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scout/build/variant/gene.py,sha256=Fj_ouJtNAZOvxYVo9oVXaYJE5_zx-mJqL-uOARD4ku8,3857
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scout/build/variant/genotype.py,sha256=QDTZWFB8ix9Zd1m9UPWgT008i6rC7gT-uFzRr9GniDU,1009
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scout/build/variant/transcript.py,sha256=hf_led1kdT3hVEwtHdORhBSk6a6o_zEDJ0z4ZF8IlFA,1205
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scout/build/variant/variant.py,sha256=
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scout/build/variant/variant.py,sha256=KHBf5dZt3i0tz8pN4Bujp7edI754cnb5jN4wcsTesVc,18740
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scout/commands/__init__.py,sha256=VrenBj1daCAnIsBZtvdbv1SuxmODT_TTY8YcxWItrXE,22
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scout/commands/base.py,sha256=WmUko96zsPbC3cUIezy0CAOOGKBFU-BoW-BPAhLORCE,4610
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scout/commands/convert.py,sha256=T5dkFjRKSTf7dBS9uKIW4wEmdL13vKzKTLRy4nvf6Vg,1090
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@@ -62,7 +62,7 @@ scout/commands/delete/__init__.py,sha256=6Z97FsWMqyKqF64Anl1zwljVNTfjJUCI7yylxIE
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scout/commands/delete/delete_command.py,sha256=c-cWdtc0VCLVLL5hpMxSuyaBiYCppm403eRoLhD1SSo,14568
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scout/commands/download/__init__.py,sha256=mfDzxqKzJ0LgfPBN_fehkdX5BPy1FJ3rauA3ORLIjCM,39
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scout/commands/download/download_command.py,sha256=m5CKefst3qhs4urfNu1A2TERisUb_5WPn-wn9bGCDr0,736
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scout/commands/download/ensembl.py,sha256=
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scout/commands/download/ensembl.py,sha256=Zr3seYt9DiadiJrGUTDcnuiopIO1PVFDDurP_sWg6Mg,2644
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scout/commands/download/everything.py,sha256=KJ0xKeIx7Rtxv38XRE2RVYBTqec9UXh6LKrozj_6Mwo,1426
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scout/commands/download/exac.py,sha256=Hy-RKnjlPRvvMgkExpyrxdjFXW_kPUvS012SyqYp41E,1052
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scout/commands/download/hgnc.py,sha256=Htp0uOhHDAqSrfIG7xRg2WE8ZKO00chOwW1xqv-OzC8,890
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@@ -103,11 +103,11 @@ scout/commands/update/compounds.py,sha256=vwCtb6045tGovKWHqY_uL8w1l9rZ_Hxlt0gUU0
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scout/commands/update/disease.py,sha256=AajPLoEtd9YeU3jf7S7ZQRs3_o1H3GSxHsST_sVaIZQ,3846
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scout/commands/update/genes.py,sha256=GhYIn2zWrAZMhdJjzzrpo8AquFqr7XOvosOk8lg4Zwk,6989
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scout/commands/update/hpo.py,sha256=eyCuUlUwPmyP0oLh1olXhdqInlUXDdLe8ylgTlHWi-g,1339
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scout/commands/update/individual.py,sha256=
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scout/commands/update/individual.py,sha256=s4HvDuAzjjs7geyUBmt8rSXpf69VWdxwK6xQj-p-oYQ,4159
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scout/commands/update/institute.py,sha256=ms8mmTGfCXqxeh_vSB1cdNDGrdHoSSgh9ryhB5GrJQc,1727
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scout/commands/update/omim.py,sha256=s39qterBGhtBfW7Uc-IJabni93PIhT8shqVbkmQBb9k,2309
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scout/commands/update/panel.py,sha256=990shZ15k5pwHUkd767o8oQ5iqVIpgRA7N_9yv1_eqc,2912
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scout/commands/update/panelapp.py,sha256=
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scout/commands/update/panelapp.py,sha256=lUDuN8iLPwUFFG_iY35L5gDEjrgsE22Eo_xB1Djj1_4,1922
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scout/commands/update/phenotype_groups.py,sha256=Ll0COlEckn1Z7VAJbFbG2EZ5FKFVEcff0sWiUsx-D-g,1980
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scout/commands/update/user.py,sha256=s5s7nh9UABBO9P6L11_j5tsi4iPxzieHw40yDhc4PWM,2497
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scout/commands/view/__init__.py,sha256=ZtRW7UBNf1rPnlCslBVcmjafOPg9WTPpn4xxlAA0wMo,23
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@@ -125,23 +125,23 @@ scout/commands/view/intervals.py,sha256=8Pofxy0DwL2Euh3SdnTLLWsU6DjLNOwIGdxeCS83
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scout/commands/view/panels.py,sha256=a0fQcP9-SDPuRYV7aEgIGUCYaMN6V47h6finpcdoomU,1098
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scout/commands/view/transcripts.py,sha256=59WyNNp7zHPJIz9QgzrkoeKaSXTtuLli0VuL8IidEmY,1277
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scout/commands/view/users.py,sha256=MKlmhDYRM7Yf-Trmi1ijEuqsDIUn326bdFADyDs7XYg,832
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scout/constants/__init__.py,sha256=
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scout/constants/__init__.py,sha256=omgOXsJ2oxjPdlQqy7teeEAsINaXH5jHTQZPG_B15p0,5918
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scout/constants/acmg.py,sha256=N9X2sJLbK6g6tDPhW0gYQifImzaowb4F6jfTYUBr-Z0,18717
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scout/constants/case_tags.py,sha256=O-BwEzU36MSpN7qqd-aSvoi4-VDRY8rM5hQ7Jg7DMgs,9447
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scout/constants/ccv.py,sha256=YP82qWCrjv3JB8d2LkUdBlBZolk0uF3nhNmkNgmebiI,9734
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scout/constants/clinvar.py,sha256=nr7KhwMIO_7taNQokRJlpgZfenMlKsdPIMpdOx3TwKY,5594
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scout/constants/clnsig.py,sha256=
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scout/constants/clnsig.py,sha256=anWIOuj_qLcDl4UsRQ50W6qlv7UaHTUbSdHOkAzL0No,1594
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scout/constants/disease_parsing.py,sha256=M9_OgsN88oXwKH_XpxdDma0zuWPRoHFQjL19tzojBPo,686
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scout/constants/file_types.py,sha256=
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scout/constants/file_types.py,sha256=9nHBnknssjdQnHm8jA8MoWAJq1shS4h5apyC9zwGCc0,2890
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scout/constants/filters.py,sha256=ZgVGt6No5D7PiN1o1wWDm3E5SCRk7YLya87_4QtIMPs,979
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scout/constants/gene_tags.py,sha256=yBrMu9qXyYaQ13l3XMakooyd2ZtPXm1XgpSSH_bC-5U,4513
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scout/constants/igv_tracks.py,sha256=
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scout/constants/igv_tracks.py,sha256=chwGmDIu45lYWix4OdmjEilCxGFHGmkdCJ-MCkRMX4s,4601
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scout/constants/indexes.py,sha256=mCj_ih9Sv7Qv4DrzLRH30EQZ-Tgyn_Sf6NYapCOlMOc,5793
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scout/constants/panels.py,sha256=
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scout/constants/panels.py,sha256=1N2Ys94IxoEWxySTJDW-rFJ55vtCkqnn6bRWjkw61J4,876
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scout/constants/phenotype.py,sha256=MrbXirisR_7GPnxV3NOj3-BoM9CvtGgFZj7PfJu85RM,2331
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scout/constants/query_terms.py,sha256=3t8JlqaM18-7t1Zd_dEv34hsIyxX_Yd6kjIbw5ZjjV8,1596
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scout/constants/so_terms.py,sha256=aJcQv3wgpZylVhqSJH854WS8xSARDxWGnW6I5mG1egE,4321
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scout/constants/variant_tags.py,sha256=
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scout/constants/variant_tags.py,sha256=NnpcJGRDycq3PIrDQsd57ynJ8NzmJETICBVjzGKZlSg,17907
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scout/constants/variants_export.py,sha256=uQvFsbRMdbgl39HUdGWzFAEe1KOHp5OgvhjbGMD3O_Q,1969
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scout/demo/643594.clinical.SV.vcf.gz,sha256=Y5CcTI7vJAS53ch8OHPR80X44rArHZoQeQZGl8AHmq0,11927
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scout/demo/643594.clinical.SV.vcf.gz.tbi,sha256=1CPB8ftoYF3gjRfqG0xMQlVMD1lY0xSdXp_KrJbfzac,1284
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scout/demo/643594.config.yaml,sha256=vHZjuZbIBluvuPeVK_nLJt63B8xVdgMlpMBoO8p3WS8,5825
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scout/load/hpo.py,sha256=ZWYjV9j6OfpI-ZZuhTQVEs_xgLa7ST2KuvYLW6ku0PY,2474
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scout/load/institute.py,sha256=etmZ0CZRHOVi3f9R-wn5BK1pZPhtZwq2QYbh2RXXxDc,625
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scout/load/panel.py,sha256=MY5M7-lDzVXt5RJH87N28TB7awdM6s-SoawholTl2GM,4776
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scout/load/panelapp.py,sha256=b37hLLpUNhXPz5SOYnhnRhb1OmSX-z2k7FtKMm9pXE8,5319
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scout/load/report.py,sha256=TJvblks6Dp5-UDflWRTa8b3fe-A4bT4QnWT2yZLhfLA,820
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scout/load/setup.py,sha256=Xu-m59rJW5bF6Agf6XdiEo_Ik4ZAFfN0tF2FjLIMYAY,8218
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scout/load/transcript.py,sha256=mk0Da7GWwqLVRp2xRD9mlzqaomH9R-TL2aKCJx4fEA8,4632
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scout/models/case/__init__.py,sha256=Sqczn7Wm9KYZtPGAHCvwX_6j9vlaK-0myJtSDlS-448,121
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scout/models/case/case.py,sha256=ENTUh3lrfc6LmOASbNDXiudDZsocHu-2LIhNz64-wPc,5295
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scout/models/case/case_loading_models.py,sha256=
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scout/models/case/case_loading_models.py,sha256=yJBt_ea-4x7SYjRiSsZtSLRGv76B_t8Lg4K68e3-kTA,22108
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scout/models/variant/__init__.py,sha256=H-IZ2hSTSVS28S8FZzA8j2Cyu1PHQFXyMWJFtCucPAk,40
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scout/models/variant/gene.py,sha256=98CG_JcAklGGFIrUulf1_olQalV65kXQO-gOf7VQZ0A,1095
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scout/server/blueprints/variants/templates/variants/utils.html,sha256=LfbWXF1A8iHKGwpkXFIzxvHlE3WahLxF6kSs050Sq2w,51741
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scout/server/extensions/__init__.py,sha256=s6qkGSFNRi_tP7yoeoXB5UarvLHidaK1Yw2Pae7Py90,1366
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scout/server/extensions/beacon_extension.py,sha256=W2dHjTWbWXLnQN3dCOzXlGX8VxSYejT_UUlEF-elh14,9901
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scout/server/extensions/bionano_extension.py,sha256=pMpnK5IkS2nzv7QrSQnfv_xJPJPoQphMUhDGp1UAXco,7109
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scout/update/panel.py,sha256=4z-vQ7GVIJXtlIub9pubFcQ-I9mLX5fRXKNPBdpuhJw,1649
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scout/utils/__init__.py,sha256=DHCMH05dxkyD7m9QSs0WXsQQPgVRFQ9XvyNeNpHjjvg,74
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scout/utils/algorithms.py,sha256=w--NauXbQohZis7obr39a8bS57C4NRelYXn79V7m1dU,800
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scout/utils/ccv.py,sha256=WhVyIzNW0ttfT4ZegOPGFR1xqqjRFNgnJSY7DPfXGNQ,5605
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scout/utils/convert.py,sha256=asrsis3zkt9jXzseRmCqSa4_t1UT73HPPQRW-DKDdqE,1794
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scout/utils/coordinates.py,sha256=n8WUFn9zohXfjxgFGryyg6mzdl0zBG8uVCdyjhizSpM,609
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scout/utils/date.py,sha256=GUALqEIgWtbopqC9wJnVKmVm5FRq111iz4RfojUIfG0,1334
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scout/utils/dict_utils.py,sha256=nstAbMYQD2KNglY69FD0qSfxYM26eM4QDpp_AqHNQ1U,251
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scout/utils/ensembl_rest_clients.py,sha256=CY2-oHP9WD0aSKXniuqr5Ch25ELXw_CsP6buQBBYssQ,2739
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scout/utils/gene.py,sha256=uzIGrPBfOkhRGGR9iTSYa00w6PWijjpzSAWRo54wixM,1430
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scout/utils/handle.py,sha256=tLjinHNLADa3IJSxMp_HJe9cbiMlPTsfky4hujplPqU,327
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scout/utils/link.py,sha256=HpQvwu0hmuCrs7TcAExLmOzEGr3glWuu8iaW0ao5pEA,9011
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scout/utils/md5.py,sha256=KkgdxOf7xbF9AF40ZjQKCgWaxFWJ9tp9RKjd8SU6IoA,649
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scout/utils/scout_requests.py,sha256=4UWE4PdpUyJ9h6CtvdrD69tQDBDTZk318-v-xHnWbEs,12796
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scout/utils/track_resources.py,sha256=eUjSEe-Ff8BIb4BHPC_COkJocQO2PaWueiPz1GAuiwY,2614
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scout_browser-4.99.0.dist-info/METADATA,sha256=TunFqZwiWX8UD4kIdLTmnVvT9hlyL8nGOvJUcSV-Gps,15526
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scout_browser-4.99.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
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scout_browser-4.99.0.dist-info/entry_points.txt,sha256=q_mxFwbMFTwXRDDIRVcqKram2ubMVmvs3CSNvZri1nY,45
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scout_browser-4.99.0.dist-info/licenses/LICENSE,sha256=TM1Y9Cqbwk55JVfxD-_bpGLtZQAeN9RovQlqHK6eOTY,1485
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scout_browser-4.99.0.dist-info/RECORD,,
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